Giovanni Palla

lasso of scatterplot plugin doesn't save back the annotation to anndata

1

it doesn't work anymore, e.g. it shows selection of axis but not axis names so it's impossible to choose which representation to visualize

the slider doesn't update the values of the scalebar

conda release fail

3

see: https://github.com/conda-forge/napari-spatialdata-feedstock/pull/1 we need to push spatialdata to conda to get this to work I think @scverse/spatialdata

https://napari.org/gallery/scale_bar.html modify example to create scalebar in the viewer for all layers (images but also layers created with the view widget)

Enable lasso selection of disjoint sets in scatterplot

1

- allow to select disjoint sets in the scatterwidget - allow to pass different labels to those (?)

modify colormap so that 0 values have alpha=0

5

saw this from @LucaMarconato tutorial on visium HD https://github.com/scverse/spatialdata-notebooks/pull/93 ```python import matplotlib.cm as cm import matplotlib.pyplot as plt import numpy as np from matplotlib.colors import LinearSegmentedColormap # modify the viridis...

### Report https://github.com/scverse/spatialdata-plot/blob/582c8379f2478d0e7bc0a7d4733d3cb6fa9af061/src/spatialdata_plot/pl/basic.py#L81 copying the entire spatialdata object can be expensive if elements are on memory. Consider change logic to avoid this. ### Version information _No response_

https://github.com/scverse/spatialdata-io/blob/e3c53b5d6789bbaec49181f33dfe368170747ce4/src/spatialdata_io/_constants/_constants.py#L247-L249 from the files on the website it doesn't look like there is such filtered counts https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-lung-cancer-if https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-intestine https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-brain-he cc @timtreis @Farbodch

store probe set for image-based transcriptomics in spatialdata

3

after discussion with @LouisK92 and @timtreis we realized it would be useful for spatialdata to also store the probe set used to target mRNA transcripts. Where should that be stored,...

omero metadata info used in napari

1

general question, but what's the scope of support of omero metadata for this napari plugin? I'm thinking for instance of: - channel ID, saved in omero metadata `labels` that could...